Error in colCenter(s.mat) : could not find function "colCenter" in running score.R

[biobug16]

Hi @jlaffy @dyammons @twoneu
While calculating score for the meta-modules by using score(), I am keep getting an error: Error in colCenter(s.mat) : could not find function "colCenter" . I tried to find a suitable library which may have a definition for colCenter(), like: library(sfsmisc), library(analogue) etc. but the error still persists.
Can you please guide how can I overcome this issue?

Thanks

[jlaffy]

Hi @biobug16,

This package has been discontinued.
Please install instead:
devtools::install_github('jlaffy/scalop')

The relevant function for scoring is
?sigScores

Thanks
Julie

[dyammons]

Hi @biobug16,
If you are trying to reproduce someone's work and must use this package, I found there is a typo in the colCenter() function that can be corrected with the following modification (see below). Otherwise, it would be best to switch to a different package, such as scalop. A little late, but hope that helps.
Best,
Dylan

#there appears to be a type-o somewhere in scrabble; need to run this function to get it to run  - taken from the source code
colCenter = function(m, by = 'mean') {
    m = as.matrix(m)
    if (by == 'mean')  by = T
    else if (by == 'median') by = matrixStats::colMedians(m)
    else stopifnot(is.numeric(by) & length(by) == ncol(m))
    scale(m, center = by, scale = F)
}